I was actually referring to the other stuff, like the Passage (4 dir) and the Ladder setting option.
The first one is unlikely, unless the auto tiles are a part of tileset A5, B, C, D, or E. But those aren't autotiles, so it's not really a possibility. I just stated it, just in case.
It doesn't look like any of the scripts would affect it (at first glance), but I'm no expert in that field.
Or...is it possible that you have an event where you set the player to have "Through ON", and maybe forgot to turn "Through" off again?